Mercurial > repos > iuc > fastq_dl

annotate fastq_dl.xml @ 2:0095a278a085 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
author iuc
date Thu, 13 Nov 2025 13:33:35 +0000
parents f1a958f3e3f6
children
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c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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1 <tool id="fastq_dl" name="fastq-dl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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2 <description>Download FASTQ files from ENA</description>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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6 <expand macro="requirements"/>
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7 <expand macro="creators"/>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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8 <command detect_errors="aggressive"><![CDATA[
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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9 mkdir -p single-end paired-end logs &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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10 #if str($input_type.select_input_type) == "accession_ids"
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11 IFS=' ' &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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12 read -ra accessionsarr <<< "$accessions" &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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13 @FASTQ_DL_FOR_LOOP@
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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14 #elif str($input_type.select_input_type) == "accessions_list"
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15 mapfile -t accessionsarr < "$accessions_file" &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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16 @FASTQ_DL_FOR_LOOP@
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17 #end if
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18 #if str($only_download_metadata) == ""
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19 &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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20 find . -maxdepth 1 -name "*_1.fastq.gz" -exec bash -c 'mv "\$0" "paired-end/\$(basename "\$0" | sed "s/_1/_forward/")"' {} \; &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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21 find . -maxdepth 1 -name "*_2.fastq.gz" -exec bash -c 'mv "\$0" "paired-end/\$(basename "\$0" | sed "s/_2/_reverse/")"' {} \; &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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22 find . -maxdepth 1 -name "*_R1.fastq.gz" -exec bash -c 'mv "\$0" "paired-end/\$(basename "\$0" | sed "s/_R1/_forward/")"' {} \; &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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23 find . -maxdepth 1 -name "*_R2.fastq.gz" -exec bash -c 'mv "\$0" "paired-end/\$(basename "\$0" | sed "s/_R2/_reverse/")"' {} \; &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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24 mv *.gz single-end > /dev/null 2>&1 || true
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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25 #end if
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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26 ]]></command>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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27 <inputs>
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28 <conditional name="input_type">
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29 <param name="select_input_type" type="select" label="Select an input type">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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30 <option value="accession_ids">ENA accession IDs</option>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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31 <option value="accessions_list">A list of ENA accession IDs, one per row</option>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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32 </param>
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33 <when value="accession_ids">
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34 <param name="accessions" type="text" label="Accession IDs" help="ENA accessions (Study, Sample, Experiment, Run accession) separated by whitespaces" optional="false" />
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35 </when>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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36 <when value="accessions_list">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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37 <param name="accessions_file" type="data" format="txt" label="Accession IDs File" help="ENA accessions (Study, Sample, Experiment, Run accession) stored in a file. One accession per line" optional="false" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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38 </when>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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39 </conditional>
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40 <param name="group_by_experiment" type="boolean" label="Group by Experiment" help="Group Runs by experiment accession" truevalue="--group-by-experiment" falsevalue="" />
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41 <param name="group_by_sample" type="boolean" label="Group by Sample" help="Group Runs by sample accession" truevalue="--group-by-sample" falsevalue="" />
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42 <param name="only_download_metadata" type="boolean" label="Only Download Metadata" help="Skip FASTQ download and retrieve metadata only" truevalue="--only-download-metadata" falsevalue="" />
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43 </inputs>
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44 <outputs>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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45 <collection name="metadata" type="list" label="Metadata files">
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46 <discover_datasets pattern="(?P&lt;designation&gt;.+)\-fastq-run-info.tsv" directory="logs" ext="tsv" />
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47 </collection>
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48 <collection name="single_end_collection" type="list" label="Single-end data">
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49 <filter>only_download_metadata == False</filter>
1
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50 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" directory="single-end" ext="fastqsanger.gz" />
0
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51 </collection>
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52 <collection name="paired_end_collection" type="list:paired" label="Paired-end data">
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53 <filter>only_download_metadata == False</filter>
1
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54 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq.gz" directory="paired-end" ext="fastqsanger.gz" />
0
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55 </collection>
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56 </outputs>
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57 <tests>
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58 <!-- #1 Testing single end and paired end using accessions file -->
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59 <test expect_num_outputs="3">
2
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60 <conditional name="input_type">
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61 <param name="select_input_type" value="accessions_list" />
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62 <param name="accessions_file" value="accessions.txt" />
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63 </conditional>
0
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64 <output_collection name="metadata" type="list" count="4">
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65 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
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66 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
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67 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
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68 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
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69 </output_collection>
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70 <output_collection name="single_end_collection" type="list" count="2">
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71 <element name="DRR011117" decompress="True">
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72 <assert_contents>
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73 <has_text text="@DRR011117.1 HXVJWSB01AD414/4" />
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74 <has_size size="23102" />
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75 </assert_contents>
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76 </element>
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77 <element name="SRR9678965" decompress="True">
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78 <assert_contents>
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79 <has_text text="@SRR9678965.1 HQCI9RE01A6I97/2" />
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80 <has_size size="2465043" />
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81 </assert_contents>
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82 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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83 </output_collection>
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84 <output_collection name="paired_end_collection" type="list:paired" count="2">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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85 <element name="ERR2651925" decompress="True">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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86 <element name="forward" decompress="True">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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87 <assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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88 <has_text text="@ERR2651925.1 M01945:48:000000000-B9G5G:1:1102:16788:1675/1" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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89 <has_size size="4977454" />
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iuc
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90 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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91 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
parents:
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92 <element name="reverse" decompress="True">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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93 <assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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94 <has_text text="@ERR2651925.1 M01945:48:000000000-B9G5G:1:1102:16788:1675/2" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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95 <has_size size="6079979" />
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96 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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97 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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98 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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99 <element name="ERR4319712" decompress="True">
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100 <element name="forward" decompress="True">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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101 <assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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102 <has_text text="@ERR4319712.1 M02944:93:000000000-ALWFJ:1:2105:13646:2309/1" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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103 <has_size size="2104680" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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104 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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105 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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106 <element name="reverse" decompress="True">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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107 <assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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108 <has_text text="@ERR4319712.1 M02944:93:000000000-ALWFJ:1:2105:13646:2309/2" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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109 <has_size size="2578613" />
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110 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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111 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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112 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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113 </output_collection>
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114 </test>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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115 <!-- #2 Testing single end and paired end using accessions as text input -->
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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116 <test expect_num_outputs="3">
2
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117 <conditional name="input_type">
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118 <param name="select_input_type" value="accession_ids" />
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119 <param name="accessions" value="ERR4319712 DRR011117 ERR2651925 SRR9678965" />
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iuc
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120 </conditional>
0
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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121 <output_collection name="metadata" type="list" count="4">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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122 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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123 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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124 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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125 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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126 </output_collection>
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127 <output_collection name="single_end_collection" type="list" count="2">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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128 <element name="DRR011117">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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129 <assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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130 <has_size size="23102" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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131 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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132 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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133 <element name="SRR9678965">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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134 <assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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135 <has_size size="2465043" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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136 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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137 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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138 </output_collection>
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139 <output_collection name="paired_end_collection" type="list:paired" count="2">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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140 <element name="ERR2651925">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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141 <element name="forward">
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142 <assert_contents>
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143 <has_size size="4977454" />
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144 </assert_contents>
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145 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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146 <element name="reverse">
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147 <assert_contents>
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148 <has_size size="6079979" />
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149 </assert_contents>
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150 </element>
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151 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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152 <element name="ERR4319712">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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153 <element name="forward">
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154 <assert_contents>
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155 <has_size size="2104680" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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156 </assert_contents>
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157 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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158 <element name="reverse">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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159 <assert_contents>
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160 <has_size size="2578613" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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161 </assert_contents>
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162 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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163 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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164 </output_collection>
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165 </test>
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166 <!-- #3 Testing only download metadata -->
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167 <test expect_num_outputs="1">
2
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diff changeset
168 <conditional name="input_type">
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169 <param name="select_input_type" value="accessions_list" />
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170 <param name="accessions_file" value="accessions.txt" />
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171 </conditional>
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172 <param name="only_download_metadata" value="true" />
0
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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173 <output_collection name="metadata" type="list" count="4">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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174 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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175 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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iuc
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c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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178 </output_collection>
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179 </test>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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180 <!-- #4 Testing group by experiment -->
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181 <test expect_num_outputs="3">
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182 <conditional name="input_type">
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183 <param name="select_input_type" value="accessions_list" />
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184 <param name="accessions_file" value="accessions.txt" />
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185 </conditional>
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186 <param name="group_by_experiment" value="true" />
0
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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187 <output_collection name="metadata" type="list" count="4">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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188 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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189 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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190 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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191 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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192 </output_collection>
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193 <output_collection name="single_end_collection" type="list" count="2">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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195 <assert_contents>
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196 <has_size size="23102" />
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197 </assert_contents>
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198 </element>
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200 <assert_contents>
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201 <has_size size="2465043" />
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202 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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203 </element>
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204 </output_collection>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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205 <output_collection name="paired_end_collection" type="list:paired" count="2">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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206 <element name="ERX2668415">
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207 <element name="forward">
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208 <assert_contents>
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209 <has_size size="4977454" />
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210 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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211 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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212 <element name="reverse">
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213 <assert_contents>
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214 <has_size size="6079979" />
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215 </assert_contents>
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216 </element>
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217 </element>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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220 <assert_contents>
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222 </assert_contents>
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223 </element>
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iuc
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225 <assert_contents>
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226 <has_size size="2578613" />
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227 </assert_contents>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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228 </element>
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229 </element>
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230 </output_collection>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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231 </test>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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232 <!-- #5 Testing group by sample -->
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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233 <test expect_num_outputs="3">
2
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234 <conditional name="input_type">
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235 <param name="select_input_type" value="accessions_list" />
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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236 <param name="accessions_file" value="accessions.txt" />
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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237 </conditional>
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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238 <param name="group_by_sample" value="true" />
0
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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239 <output_collection name="metadata" type="list" count="4">
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240 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
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241 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
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242 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
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243 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
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244 </output_collection>
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245 <output_collection name="single_end_collection" type="list" count="2">
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246 <element name="SAMD00008419">
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247 <assert_contents>
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248 <has_size size="23102" />
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249 </assert_contents>
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250 </element>
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252 <assert_contents>
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iuc
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253 <has_size size="2465043" />
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254 </assert_contents>
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255 </element>
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256 </output_collection>
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257 <output_collection name="paired_end_collection" type="list:paired" count="2">
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iuc
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259 <element name="forward">
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260 <assert_contents>
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261 <has_size size="4977454" />
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262 </assert_contents>
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263 </element>
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264 <element name="reverse">
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265 <assert_contents>
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266 <has_size size="6079979" />
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267 </assert_contents>
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268 </element>
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269 </element>
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270 <element name="SAMEA7040559">
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271 <element name="forward">
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272 <assert_contents>
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273 <has_size size="2104680" />
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274 </assert_contents>
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275 </element>
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276 <element name="reverse">
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277 <assert_contents>
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278 <has_size size="2578613" />
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279 </assert_contents>
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280 </element>
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281 </element>
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282 </output_collection>
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283 </test>
2
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284 <!-- #6 Testing exit code capture in the for loop -->
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285 <test expect_exit_code="1" expect_failure="true">
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286 <conditional name="input_type">
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287 <param name="select_input_type" value="accession_ids" />
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288 <param name="accessions" value="DRR0117 ERR2651925" />
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289 </conditional>
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290 <assert_stderr>
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291 <has_text text="fastq-dl failed for accession: DRR0117" />
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292 </assert_stderr>
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293 </test>
0
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294 </tests>
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295 <help><![CDATA[
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296
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297 This tool downloads FASTQ files from the European Nucleotide Archive (ENA) based on a list of ENA accession IDs.
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298 You can provide either accession IDs in text format or upload a file containing accession IDs (one per line).
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299 The tool also allows you to group downloaded data by experiment or sample and can optionally retrieve only metadata
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300 without downloading the FASTQ files.
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301
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302 Input Types
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303 -----------
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304
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305 You can select from two types of inputs:
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306
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307 1. **ENA Accession IDs (Text Input)**:
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308 - Provide a list of ENA accession IDs (e.g., Study, Sample, Experiment, or Run accessions) separated by whitespace.
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309
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310 2. **Accession IDs File**:
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311 - Provide a file containing a list of ENA accession IDs, one per line.
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312
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313 Parameters
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314 ----------
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315
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316 - **Group by Experiment**:
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317 This option groups the downloaded runs by the experiment accession, which can be useful if you need to process
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318 data related to a specific experiment.
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319
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320 - **Group by Sample**:
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321 This option groups the downloaded runs by the sample accession.
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322
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323 - **Only Download Metadata**:
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324 Select this option if you only want to retrieve metadata without downloading the actual FASTQ files. This is
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325 useful if you need information about the runs but do not need the raw sequence data.
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326
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327 Outputs
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328 -------
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329
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330 The tool generates three types of outputs:
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331
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332 1. **Metadata Files**:
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333 This collection contains metadata files for each accession, in `.tsv` format, which provide details about the
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334 corresponding run.
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335
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336 2. **Single-End Data**:
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337 If the input FASTQ files contain single-end reads, those files will be placed into a separate collection.
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338 In `.fastq.gz` format.
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339
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340 3. **Paired-End Data**:
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341 If the input FASTQ files contain paired-end reads, those files will be grouped into pairs (forward and reverse).
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342 The paired files will also be placed in a separate collection and will be in `.fastq.gz` format.
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343
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344 ]]></help>
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345 <expand macro="citations"/>
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346 </tool>